Hi Johan,sorry it didn't work for you.The automatic upgrade is needed because lots of changes happened in the new version, so it's better to have the automatic update.But if you want the manual update there are a few things you have to do:

1 - change your custom skin in order to have it self-contained (hopefully the upgrade process got it right about this, so you can just copy what it did for you)haacked.com/.../subtext-skin-improvements.aspx2 - delete everything you have on the subtext folder (except the Images folder) and replace it with a new installation of Subtext3 - do a manual comparison between your old web.config and the new one